- galaxy-user - lists.galaxyproject.org

Job En-queued, but not running
by Vijaykant N 31 Jul '12

31 Jul '12

Hi, I created a workflow ( https://main.g2.bx.psu.edu/u/vijay-uky/w/rna-seq-analysis ) and uploaded the reference genome (30 MB FASTA file) and the reads (45B FASTQ file after running the FASTQ groomer). Once I ran the workflow on the public server, it will enqueue the needed output (steps) but the job just wouldn't run. I tried to run the same on a local instance at my lab, it works fine. Was curious to know if there is some issue with running tools such as TopHat, Cufflinks and Cuffcompare. If you could let me know, would greatly appreciate. Sincerely, Vijay

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galaxy wiki error
by lufang0411＠sina.com 29 Jul '12

29 Jul '12

Hi I find an error in the galaxy wiki page. please see "Admin/Datatypes/Adding Datatypes" which URL is http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes <datatype extension="foo" type="galaxy.datatypes.tabular.Foobar" display_in_upload="true"/><sniffer type="galaxy.datatypes.tabular.Foobar"/> I guess there should be ":" between "tbular" and "Foobar" not "."

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tophat output spice junction output
by i b 29 Jul '12

29 Jul '12

Hi, where can I find an explanation of the columns in the splice junctions output? From 7 to12 they are only numbered thanks, ib

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flaking regions across TSS
by shamsher jagat 29 Jul '12

29 Jul '12

I am interested in getting regions flanking TSS, I am using Glaxaxy and have downloaded TSS sites using this post steps https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html Now what I would like to do is to get 5000 bp upstream an downstream using flank tool in galaxy, but i realize it only gave me option for gene start or whole gene. Is it possible to extract 5000 bp upstream and downstream regions across tss start site . Once I have that then I want to find non overlaping genes in my regions from chipseq data. Thanks Kanwar

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cuffdiff biological replicates
by i b 29 Jul '12

29 Jul '12

Hi guys, a bit of confusion about how to give cuffdiff certain outputs: having 1 control and 8 tumour samples which I consider biological replicates (not technical replicates), how shall give the input to cuffdiff? If I want to use cuffcompare as gtf: shall I cuffcompare all 8samples plus the control and then run cuffdiff using this gtf? When adding the bam files, shall I have to make 8 groups plus control groups? or one groups with 8 bams and second group with the control bam? Much appreciated an answer!! Thanks ib

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cuffdiff: same gene listed with different FPKM values
by i b 28 Jul '12

28 Jul '12

Dear all, has anything like this happened to you? I compared two samples with cuffdiff and when I look at the differentially expressed genes values I have the same gene listed for 5 times with different values. E.g. sample1 sample2 gene 71.6837 9.76435 NM_005514 87.6456 27.3965 NM_005514 115.333 4.81687 NM_005514 38.1879 5.2753 NM_005514 69.4197 5.84387 NM_005514 112.964 3.89226 NM_005514 What does this mean? And how do I know which one represents the real expression level for that gene for the two samples? Thanks, ib

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gene or transcript differential expression testing
by i b 28 Jul '12

28 Jul '12

Hi, I am a bit confused about two outputs of cuffdiff: If I want to see if two samples, e.g. treated and un-treated express similar protein levels, what would be best to look at gene differential expression or transcript diff. expression? Thanks, ib

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metagenomic workflow
by Asuncion Lago 27 Jul '12

27 Jul '12

Hi, I am trying to analyse my eukaryotic metagenome data using yours workflow for windshield splatter analysis. But I find several problems: 1- it is related to "draw phylogeny", this tool fails always for most of my samples, reporting the error: incorrect tree structure. Tree string position 341 2- It is related with the "summarize taxonomy" step. I this case I obtain results but the number of counts are too high compared with the original reads. My samples are small, around 8000 reads and the counts obtained are more that 200000 for some phyla. I guess this is not ok, as far as I understand from your paper than counts are equivalent to reads, am I right? 3- another strange thing is the fact that the number of sequences increase after run the step for select the high quality segments. Any reason for this??? I will really appreciate you help. Thanks in advance Asun

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SAM Tools Pileup
by So, Kathy GZ/US 26 Jul '12

26 Jul '12

Hi, I'm having trouble with the Generate Pileup tool and hope that you could help me troubleshoot this. I ran the tool successfully with the following options: * Use built-in index * Print the mapping quality as the last column * Print all lines * Cap mapping quality = 60 * Call consensus = yes, then default parameters The reference bases of the entire pileup file, however, are all "N." I double checked and the all the files have the same reference genome (mm9). Do you have any ideas on what went wrong? Thanks very much for your help, Kathy Kathy So Genzyme Corp. Functional Genomics 49 New York Ave. Framingham, MA 01701 508-271-4717

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The GATK has a new website and forum
by Geraldine Van der Auwera 26 Jul '12

26 Jul '12

Hi everyone, Just a quick email to let you know that the GATK has a new website and forum. The new website, released in parallel with GATK version 2.0 (beta) features a much improved documentation system and user-friendly introductory materials for new users. Also, the forum is now integrated into the website and linked to the documentation, making it much easier to refer to the docs in forum discussions and find relevant information. If you hated the old Wiki, you're going to love this. http://www.broadinstitute.org/gatk/

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